SMTL ID : 8hfy.1

SARS-CoV-2 Omicron BA.1 spike protein receptor-binding domain in complex with white-tailed deer ACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain B: N.35, T.37, E.39, N.40, R.321 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 3 residues within 4Å: Chain B: A.401, S.526, N.527 No protein-ligand interaction detected (PLIP)

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 4 residues within 4Å: Chain A: D.7, N.11, V.35, N.38 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.7 Hydrogen bonds: A:N.11, A:N.38 NAG.4: 2 residues within 4Å: Chain B: N.413, E.414 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain B: N.280 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain B: N.72 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 3 residues within 4Å: Chain B: H.355, H.359, E.383 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.355, B:H.359, B:E.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, P. et al., Structural basis of white-tailed deer, Odocoileus virginianus , ACE2 recognizing all the SARS-CoV-2 variants of concern with high affinity. J.Virol. (2023)

Release Date

2023-08-30

Peptides

Spike protein S1: A
Angiotensin-converting enzyme: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Spike protein S1

Angiotensin-converting enzyme